wwPDB Policies and Processing Procedures Document
Section A: wwPDB Policies
Authored by the wwPDB annotation staff
Apr 2024 version 5.3

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Table of Contents
1 PDB Entry Requirements ........................................................................................ 4
2 Entry Authorship ..................................................................................................... 83 Release of PDB Entries ........................................................................................... 9
4 Assignment of PDB IDs and Ligand codes ......................................................... 11
5 Changes to Entries ................................................................................................ 11

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2Preface
This document outlines the annotation procedures and policies of the wwPDB. Given thecomplex nature of some of the issues that can arise during processing, exceptions to policy are
considered on a case-by-case basis by the wwPDB Directors/Heads.
The two sections in the complete document are:
A: wwPDB policies
B: wwPDB processing procedures
Further information about these sections is available in the introduction to each section.
Sept. 2021: major version 5.0, make contact info for entry PI(s) public.

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31 PDB Entry Requirements
What are the requirements of acceptance of an entry to the PDB?
OneDep depositions
The wwPDB will accept all experimentally determined structures of biological macromoleculesthat meet the minimum requirements. These requirements include: three-dimensional atomic
coordinates, information about the composition of the structure (studied sample sequence(s),source organism(s), molecule name(s), chemistry, etc.), information about the experiment
performed, details of the structure determination steps and author contact information are also
necessary for the deposition. In addition, structure factor or intensity data are required for X-ray
submissions, restraints and chemical shifts are required for NMR submissions. Map volume
deposition to EMDB is mandatory for PDB depositions of 3DEM models. If the experimental
data deposited with the model coordinates does not follow traditional processing procedures
then raw data should be made available by providing a DOI assigned by the existing archives
for raw experimental data (eg SBGrid or IRRMC).
Mandatory X-ray structure factor data and NMR restraint data deposition started from Feb 1st,
2008. Mandatory NMR chemical shift data deposition started from Dec 6th, 2020. Mandatory
EM map volume deposition started from Sep 5th, 2016.
For structures determined by X-ray crystallography, all atoms must have full B factors. If TLS
was used during refinement, the residual B factors must be converted to full B factors. All atoms
described by TLS records must have associated ANISOU records.
On occasion, the wwPDB is asked to archive a structure that was determined before depositionof experimental data became mandatory and the experimental data are no longer available. It isdifficult to validate such structures without experimental data.
In such cases, the wwPDB Directors/Heads will determine if the structure can be deposited to
the PDB. Criteria for accepting structures determined by experimental methods but without
experimental data are as follows: there is a peer-reviewed publication prior to January 1st 2008
describing the corresponding structure(s) and either the polymer sequence and/or entities are
not represented in the PDB archive or the deposition includes one or more ligand(s) not
currently represented in the PDB Chemical Component Dictionary.

Deposition of integrative structures
Integrative structures of biological macromolecular systems are computed by combining
different types of information, including varied experimental data, physical theories, statisticalpreferences, and/or prior models. Experimental data can be produced by traditional structure
determination methods (i.e., macromolecular X-ray crystallography (MX), Nuclear Magnetic
Resonance (NMR) spectroscopy, and three-dimensional Electron Microscopy (3DEM)), as wellas other biophysical and proteomics methods such as small angle scattering (SAS), atomic force
microscopy (AFM), chemical crosslinking with mass spectrometry, Förster resonance energy
transfer (FRET) spectroscopy, electron paramagnetic resonance (EPR) spectroscopy, andHydrogen/Deuterium exchange (HDX) with mass spectrometry or NMR spectroscopy.
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The PDB accepts integrative structures of biological macromolecules that are at least partly
based on experimental data, via the PDB-IHM (PDB-Dev) system. An integrative structure canbe depicted using a flexible model representation, including ensembles of multi-scale, multistate, and ordered models. In addition to atomic and/or coarse-grained coordinates of themodeled system, the deposition needs to include starting models, spatial restraints, modelingprotocols, as well as specific metadata information (e.g., citations, authors, software, relevant
data in external repositories, and reference sequence information).

What types of experimentally-determined structures are accepted by the wwPDB?
Since October 15, 2006, PDB depositions have been restricted to atomic coordinates that aresubstantially determined by experimental measurements on actual sample specimens containing
biological macromolecules1. Currently, coordinate sets produced by X-ray crystallography, NMR,
electron microscopy, neutron diffraction, powder diffraction, and fiber diffraction can be deposited
to the PDB, provided the molecule studied meets the minimum size requirement.
Use of non-crystallographic symmetry (NCS):
For crystal structures, coordinates for the complete asymmetric unit should be provided, even if
non-crystallographic symmetry (NCS) is used. The only exceptions are models that produce
highly symmetric assemblies (e.g., viruses, helical symmetry, etc.) in which only a portion of theasymmetric unit is used in refinement. Depositors must provide the model in the standard
crystal frame along with the NCS matrices.
For microscopy methods, if symmetry operators are required to create the complete biologicalassembly from the modeled coordinates, such operators must be provided.
Example: in PDB entry 2wbh, the complete MS2 bacteriophage capsid biological assembly is
generated from the three deposited chains (A, B, C) by applying the 60 operators provided in_pdbx_struct_oper_list (REMARK 350) records. The crystal asymmetric unit of 2wbh, whichcorresponds to 1/3rd of the complete capsid, is generated from the three deposited chains byapplying the 20 NCS operations provided in the _struct_ncs_oper (MTRIX) records.
ftp://ftp.wwpdb.org/pub/pdb/data/structures/divided/pdb/wb/pdb2wbh.ent.gz
ftp://ftp.wwpdb.org/pub/pdb/data/structures/divided/mmCIF/wb/2wbh.cif.gz
Theoretical model depositions determined purely in silico using, for example, homology or ab initio
methods, are no longer accepted.
Theoretical models that have been previously released or those that were deposited before
October 15, 2006 will continue to be publicly available via the historical models archive at
ftp://ftp.wwpdb.org/pub/pdb/data/structures/models/.
Structures determined by methods not currently supported by the PDB will be reviewed inconsultation with community of experts to determine if structures determined by the method
1

H.M. Berman, S.K. Burley, W. Chiu, A. Sali, A. Adzhubei, P.E. Bourne, S.H. Bryant, J. Roland L.
Dunbrack, K. Fidelis, J. Frank, A. Godzik, K. Henrick, A. Joachimiak, B. Heymann, D. Jones, J.L. Markley,
J. Moult, G.T. Montelione, C. Orengo, M.G. Rossmann, B. Rost, H. Saibil, T. Schwede, D.M. Standley,
and J.D. Westbrook (2006) Outcome of a workshop on archiving structural models of biologicalmacromolecules. Structure. 14: 1211-1217

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5should in principle be accepted by the PDB. Once such a determination is made, a new templatefor PDB entries derived from this method will be developed.

How and where are experimental data submitted?
The OneDep deposition sites for all experimental methods are available at the following wwPDB
sites:RCSB http://deposit.wwpdb.org/deposition/
PDBe https://deposit-pdbe.wwpdb.org/deposition/
PDBj http://deposit-pdbj.wwpdb.org/deposition/
For deposition of additional NMR experimental data, an access point is located at:
BMRB https://bmrb.io/deposit/
PDBj-BMRB http://deposit.bmrb.pdbj.org/

For deposition of integrative structures, access PDB-IHM (PDB-Dev) at:
https://pdb-dev.wwpdb.org/deposit.html

What are the format requirements for deposition?
To ensure that all wwPDB and related deposition tools function with minimal loss of data fidelity,
depositors should output PDBx/mmCIF format files from their refinement program, if supported.
A PDBx/mmCIF preparation guide is available. The format requirements for depositing
structures are as follows:
Coordinates and meta-data
PDBx/mmCIF format: Deposition can be prepared in PDBx/mmCIF exchange format.
Definitions and dictionary are available in HTML, ASCII, and XML format (seehttp://mmcif.wwpdb.org/ for details).
PDB format: Definitions and format content guide are available in PDF and HTML format(see http://wwpdb.org/documentation/file-format for details).
Structure factors••

The structure factor file can either be in mmCIF or mtz formats and should include h,k, l, F, SigmaF (and/or I and SigmaI) and test flags.
Definitions and format are available at
http://wwpdb.org/documentation/procedure#toc_appendicsB.

Restraint Data•

Currently there are no restrictions on the format.

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6•The common format is NMR-STAR (see https://bmrb.io/formats.shtml for details).

What types of structure can be deposited to the PDB?
Biomolecular polymers, including polypeptides, polynucleotides, polysaccharides, and theircomplexes that meet the following criteria are accepted:•

For polypeptide structures-Gene products-Naturally-occurring peptides that are non-ribosomal in origin-Peptidic repeat units of larger polymers (such as fibrous and amyloid polymers)-Synthetic peptides of at least 24 residues within a polymer chain (smaller,
biologically-relevant oligopeptides are also acceptable)• Polynucleotide structures-Of four or more residues• Polysaccharide structures-Of four or more residues
Crystal structures of peptides with fewer than 24 residues within any polymer chain that do notmeet the criteria above should be deposited at the Cambridge Crystallographic Data Centre(CCDC, http://www.ccdc.cam.ac.uk/products/csd/deposit/). NMR structures of such molecules
should be submitted to Biological Magnetic Resonance Data Bank (BMRB) through the Small
Molecule Structure Deposition (SMSdep, http://smsdep.protein.osaka-u.ac.jp/bmrb-adit/) system.
Structures of smaller oligonucleotides (dinucleotides and trinucleotides) can be deposited at the
Nucleic Acid Database (NDB, http://ndbserver.rutgers.edu).
Molecules that do not conform to these guidelines, but have been previously deposited in the
PDB, will not be removed.

Can a re-refined structure be deposited to the PDB?
A re-refined structure based on the data generated by a research group or laboratory
different from the contributors can only be deposited to the PDB if there is an associatedpeer-reviewed publication available describing the details of the re-refined structure.
A re-refined entry may be deposited prior to publication, but will not be processed (willhave REFI status) or released until the associated peer-reviewed publication has become
publicly available. The depositor must provide the relevant publication details to the
wwPDB and allow for extra time required for the processing and release of these entries.
Authors who require early entry processing in order to facilitate journal manuscript
submission should contact the wwPDB and processing of these entries will be handled
on a case-by-case basis.
In addition, a dedicated remark (_pdbx_database_remark with id = 0) will be added to
the PDBx/mmCIF file along with the primary citation of the original PDB entry (under_citation with id = original_data_1).
Details on the annotation of a re-refined PDB entry can be found at
http://wwpdb.org/documentation/procedure.

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2

Entry Authorship

There are 3 types of authorship associated with a PDB entry: Entry Author, Contact Author, andCitation Author.
The supervisor of the research group where the structural determination work began, known as
the Principal Investigator (PI) or Team Leader equivalent, is responsible for the authorshiprepresented in the final PDB entry. If more than one PI/Team Leader equivalent is responsible
for the entry, they will need to come to a mutual decision on all issues.

Contact Authors
The Contact Authors indicated at the time of deposition are responsible for depositing thestructure, responding to any queries from the wwPDB during processing, and indicating whenentries can be released.
At least one Contact Author should be designated "responsible for correspondence" including
data submission and responses to questions from the wwPDB. The PI/Team Leader equivalent
must be listed as a Contact Author and will be copied on all communications. In some cases,
the PI/Team Leader equivalent may be contacted with questions directly. It is the responsibilityof the depositor to label author roles correctly.
All Contact Authors will be notified of any changes or requests for changing/obsoleting/removing
entries. In the case of a conflict between Contact Authors, the wwPDB will follow requests fromthe PI/Team Leader equivalent who ultimately makes the final decision. The PI/Team Leader
equivalent is the individual(s) specified as PI/Team Leader in the PDB entry that was approvedby the contact authors.

Entry Authors
The PI/Team Leader equivalent should be included as Entry Author. In addition, it isrecommended that all who contributed to the structural determination as identified by the
PI/Team Leader equivalent, be designated as Entry Authors. Commercial entities should include
the company name along with any other relevant names.
Entry Authors can be the same as those listed in the primary citation, or a subset of Citation
Authors. Alternatively, there may be more Entry Authors listed than there are Citation Authors.
It is the responsibility of the PI/Team Leader equivalent to ensure that the listing of Entry
Authors is appropriate and that all listed Entry Authors have approved the final version of thedata and have agreed to PDB submission.
For the entries deposited or revised starting September 24th 2021, name(s), email address(es),and ORCiD id(s) of principal investigator(s) are made publicly available when these entries are
released.

Citation Authors

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8Citation Authors are those listed on the primary publication describing the entry. The Citation
Author list may be different from the Entry Author list as described above.
If an entry is to be obsoleted, it is the responsibility of the PI/Team Leader equivalent to notify
the corresponding author of the paper.

Authorship and Re-refined Entries
A re-refinement of data available in the PDB must acknowledge the original data set by citing
the PDB entry (and corresponding citation, if available) in the re-refined PDB entry. This
information can be noted at the time of deposition. A re-refined entry may be deposited prior to
publication but will not be processed (will have REFI status) or released until the associatedpublication has become publicly available. See the wwPDB Processing Procedures Document
for further information (Section A.9).

3

Release of PDB Entries

What are the author-requested status codes for PDB entries?
REL entries are to be released as soon as the authors have approved the processed files.
HPUB (Hold until PUBlication) entries are placed on hold until publication or until one year
from the date of deposition, whichever comes first.
HOLD entries are placed on hold for up to one year from the date of deposition.

What are the release policies for PDB entries?
REL entries are scheduled for release after authors have approved the processed files. If no
reply is received within three weeks after the validation report is made available to the authors,
the wwPDB will consider the entry to have been approved by the authors. If at that point there
are no outstanding issues2 with the entry, the entry will be released. For entries with outstanding
issues see the Problem Structures section below. Entries can be released without citation
information and updated with this information at a later date.
HPUB/HOLD entries will be released either when release is requested by the authors or by ajournal, or when the wwPDB becomes aware of a publication describing the entry.
HPUB/HOLD entries cannot be held for more than one year beyond the date of deposition. If an
entry remains unreleased at the end of the hold period, it must either be released or withdrawn.
Ten months following deposition, the wwPDB will communicate with the authors of unreleased
entries, asking whether they wish to release or withdraw the entry before the one-year
anniversary of the deposition date.
Once the wwPDB is aware of a publication (electronic or print, whichever is published sooner)
describing a PDB entry, the wwPDB will neither delay the release of nor permit the withdrawal of2

Note: Any issues that arise during annotation that prevent the standard processing of submissions are
considered to be outstanding issues. These could include, for example, unusual geometry andstereochemistry, sequence-related problems, solvent structures, to name but a few.

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9that entry. Any revision of the PDB entry following release will be managed under the PDB
archival versioning system - please see the section 'What changes can be made after release?'for more details.
The wwPDB receives publication dates and citation information from authors, some journals,
and the user community. In addition, the wwPDB also scans the literature for publications. While
the wwPDB makes every effort to track citations and release entries in a timely manner, it isultimately the responsibility of the authors to notify the wwPDB when publication occurs.
Submissions to public preprint archives are deemed to be publications.
It is normal practice for authors to review and approve curated entries before they are released.
If the contact author does not reply within three weeks after the validation report is madeavailable to them, and assuming that there are no outstanding issues with the deposition, the
wwPDB will deem this entry to have been approved by the authors. The entry will be released
when the wwPDB is aware that the publication describing the entry is available. Entries withoutstanding issues will be handled as per the Problem Structures section below.
Authors may withdraw their unreleased entries, provided the publication citing the entry has notbeen published. When an entry is withdrawn, the latest version of the processed files will bemade available to the authors in case they wish to re-deposit the entry in the future. Withdrawn
entries will remain in the list of unreleased entries in the PDB archive (status WDRN).
Problem Structures, as identified by the wwPDB biocuration staff or from the contents of the
wwPDB validation report, will be discussed with the authors in order to resolve issues such as
unusual structural chemistry, distant water molecules, long/short covalent bonds, certain
sequence mismatches, or other conflicts. An entry for which these issues cannot be resolved will
be withdrawn upon expiration of the one-year hold unless a publication describing the entry isavailable. In that case, the entry will be released by wwPDB staff with a database_PDB_caveat
record. If a publication describing a withdrawn entry appears in the literature, the withdrawn statusof an entry may be reversed by the wwPDB (as determined by the wwPDB staff).

Can the experimental data be released separately from the coordinate file?
Coordinates and experimental data share the same release status (REL, HPUB, or HOLD).
Thus, coordinate and experimental data files can only be released simultaneously.

What are the deadlines for requesting release of entries?
PDB entries are processed by the members of the wwPDB (RCSB-PDB, PDBe, and PDBj). They
are either released immediately (REL), when the corresponding paper is published (HPUB), or ona particular date (HOLD).
Each week, all files scheduled for release or revision are subjected to a final data integrity check.
Contact Authors may be asked to resolve issues arising while entries are prepared for release.
When release of HPUB structures is requested, wwPDB staff routinely check for the primarycitation. To be included in the upcoming update, any required author correspondence should besent to the appropriate wwPDB member by 12:00 noon on Thursday (local time at processingsite). Occasionally the request cutoff date may be changed under certain circumstances.
Requests received after these cutoff times will be processed during a later update cycle.

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10Depositors should contact the wwPDB through the web communication within the relevant
deposition while general PDB users should contact the wwPDB at deposit-help@mail.wwpdb.org
regarding publication and/or release.
All entries set for release are transferred to the RCSB-PDB (the current Archive Keeper) for final
packaging into the master PDB ftp archive. Data entries are added to the PDB archive on a
weekly schedule and synchronized among FTP sites at RCSB-PDB, PDBe, and PDBj.
The process for weekly PDB archive data release, with the advice and concurrence of theAdvisory Committee to the Worldwide Protein Data Bank, is as follows:
Phase I: Every Saturday from 3:00 UTC, for every new entry, the following will be provided fromthe wwPDB website: sequence(s) (amino acid or nucleotide) for each distinct polymer and,
where appropriate, the InChI string(s) for each distinct ligand and the crystallization pH value(s).
Phase II: Every Wednesday from 00:00 UTC, all new and modified data entries will be updated
at each of the wwPDB FTP sites.
Revision dates (database_PDB_rev.date, pdbx_version) The revision date indicates thedate of release of the entry. Revision date will be set to the date of scheduled release, which ison Wednesday.

Who has access to unreleased data?
Unreleased coordinate sets are distributed only to the authors of that entry. Reviewers of thejournal submissions may not obtain unreleased coordinate sets from the wwPDB. The wwPDB
strongly encourages journal editors and referees to request wwPDB validation reports from
authors as part of the manuscript submission and review process.

What information is available for unreleased entries? Unreleased entries at the PDB
archive contain the title, authorship, status, PDB ID, experimental data status and sequenceavailability. Entry titles and authorship may be suppressed at the request of the Contact Author,
but status and PDB ID cannot be publicly suppressed.

4 Assignment of PDB IDs and Ligand codes
Can a PDB ID or ligand code be requested? Neither a single PDB ID/ligand code nor a
range of PDB IDs/ligand codes may be requested. The wwPDB reserves the right to change
author’s ligand codes. PDB ID and ligand codes are automatically assigned and do not carry
identifying information.

When are PDB IDs assigned? PDB IDs are automatically assigned by the deposition softwaretool, when the author has completed his/her deposition (i.e., the author has filled out at least theminimal information for deposition and has pressed the deposit & confirmation buttons.)

5 Changes to Entries
What changes can be made before release? Authors can update the coordinates,
experimental data, and related header information any time before release.

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If the depositor sends new coordinates for an entry shortly before or at the time of electronic or
paper publication, the release of the entry may be subject to delay because the file must be reprocessed.
Once an entry is marked for release, the author has until the deadline time listed above (seeSection 3, Deadline for requesting release of entries) to submit revisions or to request the entry
not to be released.

What changes can be made after release?
Minor changes may be made. These are defined as:•

Update on metadata section such as citation, author’s name, etc.

•

Update or change on structure factor or constraint file due to format corrections or additionof data set while coordinates remain unchanged.

Major revisions to coordinates that change the structure's geometry or chemical composition(such as a change in the sequence of the polymers or ligand identity) can be made throughdepositor-initiated or wwPDB-initiated updates. Major revisions include:•

Replacement of any existing coordinates (the x,y,z values themselves).

•

Changes in chemical composition (e.g., SO4→PO4 or SER→CYS).

•

Changes in coordinate section including chain ID, numbering, atom name, ordering ofmolecules and/or ligands.

•

Changes in sample sequence including add or remove a region that is unobserved in thecoordinates such as terminal or loop region.

Depositor-initiated or wwPDB-initiated update to the coordinates will be versioned while retaining
the same PDB accession code. Entries will be processed and released immediately.
If there is a change to the experimental data (they are new, or in some way modified), an entry
must be replaced by a new deposition needing a new PDB ID. The old entry is then obsoleted (ifthe depositor wishes) and replaced (superseded) by the new one.
Obsolete entries remain available to the public through the ftp archive. Users who search for an
obsolete structure through the main web search interface will be automatically redirected to thesuperseding entry. Under no circumstances can a released structure be withdrawn.
There are some rare circumstances in which an obsolete structure is not superseded by a new
structure. The entry must contain a statement specifying the reason for obsoleting the structure(under _pdbx_database_PDB_obs_spr.details).
•

The publication is retracted. The associated PDB entry will be obsoleted if requested by
the journal. If a request has not been received, the wwPDB will do its best to contact thedepositor and co-authors, (former) PIs, journal editors, etc. when made aware of theretraction. If the reason(s) for retraction were such that the associated PDB entry needs
to be made obsolete, the wwPDB will obsolete the entry. The citation in the obsoleted
entry is the published journal retraction.

•

There is no associated publication and the entry author obsoletes the entry (e.g., thestructure is incorrect).

•

A third-party (such as the employer) requests that the entry is obsoleted (e.g., in case of
malfeasance). In such cases, the wwPDB will obsolete the entry if either the primary

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12citation for the structure is retracted or a formal report by an appropriate government or
supranational agency in the region (e.g., US Office of Research Integrity) is published.
wwPDB Remediation
The wwPDB reviews the entire archive on a regular basis and remediates PDB data as required.
The coordinates themselves are never changed, but there may be changes in the meta data andnomenclature to assure consistency and uniformity in the files. The nature of the changes is
described in a public document on the wwPDB site. In the case of global remediation, theindividual authors are not contacted. A version number is assigned and recorded in_pdbx_version mmCIF category in every file. The older version is maintained as a snapshot on
the FTP site.

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